Add TLDR module - Revision history

Khtang: /* Add job type into psql table */

2025-01-14T18:12:11Z

Add job type into psql table

← Older revision		Revision as of 18:12, 14 January 2025
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	* Insert new job type (Please be extra careful when doing this step)		* Insert new job type (Please be extra careful when doing this step)
	'''This is important to start command with 'begin;' so that if any syntax mistakes could be undo.'''		'''This is important to start command with 'begin;' so that if any syntax mistakes could be undo.'''
	blaster=> begin; insert into job_types values(<next_available_id>, now(), '<~~your_job_name~~>');		blaster=> begin; insert into job_types values(<next_available_id>, now(), '<job_shortname>', true, false, 1, <description>);
	Example:		Example:
	blaster=> begin; insert into job_types values(16, now(), 'shape');		blaster=> begin; insert into job_types values(16, now(), 'shape', true, false, 1, 'look up molecule based on molecular shape using FastROCS');
	//To save data		//To save data
	blaster=> commit;		blaster=> commit;

Khtang: /* Add job type into psql table */

2025-01-14T17:38:17Z

Add job type into psql table

← Older revision		Revision as of 17:38, 14 January 2025
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	You will see table like this		You will see table like this
	job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description		job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description
	------------+----------------------------+----------------------+--------+-------------------+--------------------+~~----------~~------------------------------------------------------------------------------------------------		------------+----------------------------+----------------------+--------+-------------------+--------------------+------------------------------------------------------------------------------------------------
	34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.		34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.
	33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.		33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.

Khtang: /* Add job type into psql table */

2025-01-14T17:38:08Z

Add job type into psql table

← Older revision		Revision as of 17:38, 14 January 2025
Line 10:		Line 10:
	You will see table like this		You will see table like this
	job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description		job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description
	------------+----------------------------+----------------------+--------+-------------------+--------------------+~~---------------~~----------------------------------------------------------------------------------------------------------		------------+----------------------------+----------------------+--------+-------------------+--------------------+----------------------------------------------------------------------------------------------------------
	34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.		34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.
	33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.		33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.

Khtang at 17:37, 14 January 2025

2025-01-14T17:37:53Z

← Older revision		Revision as of 17:37, 14 January 2025
Line 9:		Line 9:
	blaster=> select * from job_types order by job_type_id;		blaster=> select * from job_types order by job_type_id;
	You will see table like this		You will see table like this
	job_type_id \| last_updated \| short_name		job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description
	-------------+----------------------------+-------------------		------------+----------------------------+----------------------+--------+-------------------+--------------------+-------------------------------------------------------------------------------------------------------------------------
	~~1 \| 2018~~-10-~~05 00:00:00 \| analog~~		34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.
	~~2 \| 2018~~-10-~~05 00:00:00 \| blaster~~		33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.
	~~3 \| 2018~~-10-~~05 00:00:00 \| blasterpdb~~
	~~4 \| 2018~~-10-~~05 00:00:00 \| build2d~~
	~~5 \| 2018~~-10-~~05 00:00:00 \| build3d~~
	~~6 \| 2018~~-10-~~05 00:00:00 \| cluster~~
	~~7 \| 2018~~-10-~~05 00:00:00 \| covalent~~
	~~8 \| 2018~~-10-~~05 00:00:00 \| dude~~
	~~9 \| 2018~~-10-~~05 00:00:00 \| libanalysis~~
	10 \| ~~2018~~-10-~~05 00~~:00:00 \| ~~reaction~~
	11 \| ~~2018-10-05 00:00:00~~ \| ~~sea~~
	12 \| ~~2018-10-05 00:00:00~~ \| ~~threec~~
	13 \| ~~2018~~-10~~-05 00~~:00:00 \| ~~transform~~
	14 \| ~~2018-10-05 00:00:00~~ \| ~~zincbatch~~
	15 \| ~~2018-12-01 18:47:34~~ \| ~~cluster_molecules~~

	* Insert new job type (Please be extra careful when doing this step)		* Insert new job type (Please be extra careful when doing this step)

Khtang: /* Setting up templates */

2025-01-14T17:17:40Z

Setting up templates

← Older revision		Revision as of 17:17, 14 January 2025
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	su - www		su - www
	cd /nfs/ex7/blaster/templates/		cd /nfs/ex7/blaster/templates/
	mkdir <job_name> // job_name must match the shortname in job_types table		mkdir <job_name> # job_name must match the shortname in job_types table
	chmod 777 job_name //for now...		chmod 777 job_name #for now...
	* Get parameters.json		* Get parameters.json
	This is recommend that you go though all the currently existing modules on [https://tldr.docking.org TLDR] and reuse instead of starting one from scratch.		This is recommend that you go though all the currently existing modules on [https://tldr.docking.org TLDR] and reuse instead of starting one from scratch.

Khtang at 07:52, 14 January 2025

2025-01-14T07:52:12Z

← Older revision		Revision as of 07:52, 14 January 2025
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	Here is quick guide to add your script into [[~~Tools18~~]] interface		Here is quick guide to add your script into [[TLDR]] interface
	=== Scripts ===		=== Scripts ===

Khtang: Khtang moved page Add Tools18 module to Add TLDR module without leaving a redirect

2025-01-14T07:51:58Z

Khtang moved page Add Tools18 module to Add TLDR module without leaving a redirect

← Older revision

Revision as of 07:51, 14 January 2025

Khtang: /* Setting up templates */

2025-01-14T07:51:28Z

Setting up templates

← Older revision		Revision as of 07:51, 14 January 2025
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	=== Setting up templates ===		=== Setting up templates ===
	* Create directory		* Create template directory
	$ cd /nfs/ex7/blaster/templates/		sudo -i
	$ mkdir <job_name> // job_name must match the shortname in job_types table		su - www
	$ chmod 777 job_name //for now...		cd /nfs/ex7/blaster/templates/
			mkdir <job_name> // job_name must match the shortname in job_types table
			chmod 777 job_name //for now...
	* Get parameters.json		* Get parameters.json
	This is recommend that you go though all the currently existing modules on [https://tldr.docking.org TLDR] and reuse instead of starting one from scratch.		This is recommend that you go though all the currently existing modules on [https://tldr.docking.org TLDR] and reuse instead of starting one from scratch.
	$ cd job_name		cd job_name
	$ cp <whatever parameters.json you pick>		cp <whatever parameters.json you pick>
	$ vim parameters.json		vim parameters.json
	Change the variables. Check on the website if the module shows up.		Change the variables. Check on the website if the module shows up.
	* Move your shell scripts in directory		* Move your shell scripts in directory

Khtang: /* Add job type into psql table */

2025-01-14T07:44:18Z

Add job type into psql table

← Older revision		Revision as of 07:44, 14 January 2025
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	//To save data		//To save data
	blaster=> commit;		blaster=> commit;
	//Or if made mistake, to ~~reserve~~ cmd		//Or if made mistake, to reverse cmd
	blaster=> rollback;		blaster=> rollback;

Btingle at 19:30, 18 October 2022

2022-10-18T19:30:13Z

← Older revision		Revision as of 19:30, 18 October 2022
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	=== Add job type into psql table ===		=== Add job type into psql table ===
	*Access the database		*Access the database
	$ psql -h ~~mem~~ blaster blasteruser		$ psql -h mem2 -d blaster -U blasteruser

	*Look for the next available index on job_types table		*Look for the next available index on job_types table

← Older revision		Revision as of 17:37, 14 January 2025
Line 9:		Line 9:
	blaster=> select * from job_types order by job_type_id;		blaster=> select * from job_types order by job_type_id;
	You will see table like this		You will see table like this
	job_type_id \| last_updated \| short_name		job_type_id \| last_updated \| short_name \| hidden \| approval_required \| job_type_status_fk \| description
	-------------+----------------------------+-------------------		------------+----------------------------+----------------------+--------+-------------------+--------------------+-------------------------------------------------------------------------------------------------------------------------
	~~1 \| 2018~~-10-~~05 00:00:00 \| analog~~		34 \| 2024-03-07 09:48:22.442957 \| build3d_covalent \| f \| f \| 2 \| Build db2 for covalent library using DOCK3.7 pipeline.
	~~2 \| 2018~~-10-~~05 00:00:00 \| blaster~~		33 \| 2023-02-08 10:17:11.904655 \| dockopt2 \| t \| f \| 3 \| Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.
	~~3 \| 2018~~-10-~~05 00:00:00 \| blasterpdb~~
	~~4 \| 2018~~-10-~~05 00:00:00 \| build2d~~
	~~5 \| 2018~~-10-~~05 00:00:00 \| build3d~~
	~~6 \| 2018~~-10-~~05 00:00:00 \| cluster~~
	~~7 \| 2018~~-10-~~05 00:00:00 \| covalent~~
	~~8 \| 2018~~-10-~~05 00:00:00 \| dude~~
	~~9 \| 2018~~-10-~~05 00:00:00 \| libanalysis~~
	10 \| ~~2018~~-10-~~05 00~~:00:00 \| ~~reaction~~
	11 \| ~~2018-10-05 00:00:00~~ \| ~~sea~~
	12 \| ~~2018-10-05 00:00:00~~ \| ~~threec~~
	13 \| ~~2018~~-10~~-05 00~~:00:00 \| ~~transform~~
	14 \| ~~2018-10-05 00:00:00~~ \| ~~zincbatch~~
	15 \| ~~2018-12-01 18:47:34~~ \| ~~cluster_molecules~~

	* Insert new job type (Please be extra careful when doing this step)		* Insert new job type (Please be extra careful when doing this step)